Olivier Duss

European Molecular Biology Laboratory

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Frédéric H.‐T. Allain

ETH Zurich

Mario Schubert

ETH Zurich

James R. Williamson

Scripps Research Institute

Erich Michel

University of Zurich

Joseph D. Puglisi

Stanford University

Galina A. Stepanyuk

Cyrus Biotechnology

Nusrat S. Qureshi

European Molecular Biology Laboratory

Maxim Yulikov

ETH Zurich

N. Diarra dit Konte

ETH Zurich

Gunnar Jeschke

ETH Zurich

Cooperative Institutions

ETH Zurich

European Molecular Biology Laboratory

Heidelberg University

University of Zurich

Centre National de la Recherche Scientifique

Board of the Swiss Federal Institutes of Technology

École Polytechnique Fédérale de Lausanne

Stanford University

European Molecular Biology Organization

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Tracking transcription–translation coupling in real time

Nature (2024)

Nusrat S. Qureshi Olivier Duss

Transcription

Ribosome profiling

10.1038/s41586-024-08308-w

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Citations (4)

Structural basis of the non-coding RNA RsmZ acting as a protein sponge

Nature (2014)

Olivier Duss Erich Michel Maxim Yulikov Mario Schubert Gunnar Jeschke

Sponge

10.1038/nature13271

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Citations (194)

Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding

Cell (2019)

Olivier Duss Galina A. Stepanyuk Joseph D. Puglisi James R. Williamson

Ribosomal protein

5.8S ribosomal RNA

Folding (DSP implementation)

10.1016/j.cell.2019.10.035

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Citations (88)

Co‐transcriptional assembly mechanisms of protein‐RNA complexes

FEBS Letters (2023)

Nusrat S. Qureshi Olivier Duss

This graphical review provides a mechanistic overview of different molecular processes that are tightly coupled and cooperate to achieve efficient and spatial‐temporally regulated co‐transcriptional protein‐RNA complex assembly, including co‐transcriptional RNA folding, processing, modification and the assembly in context of biomolecular condensates.

Folding (DSP implementation)

10.1002/1873-3468.14758

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Citations (4)

Real-time tracking of transcription-translation coupling

Biophysical Journal (2023)

Nusrat S. Qureshi Olivier Duss

Transcription

Ribosome profiling

Bacterial transcription

10.1016/j.bpj.2022.11.2608

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Citations (1)

Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination

Nature Communications (2017)

N. Diarra dit Konte Miroslav Krepl Fred F. Damberger Nina Ripin Olivier Duss

Abstract The cyclooxygenase-2 is a pro-inflammatory and cancer marker, whose mRNA stability and translation is regulated by the CUG-binding protein 2 interacting with AU-rich sequences in the 3′ untranslated region. Here, we present the solution NMR structure of CUG-binding protein 2 RRM3 in complex with 5′-UUUAA-3′ originating from the COX-2 3′-UTR. We show that RRM3 uses the same binding surface and protein moieties to interact with AU- and UG-rich RNA motifs, binding with low and high affinity, respectively. Using NMR spectroscopy, isothermal titration calorimetry and molecular dynamics simulations, we demonstrate that distinct sub-states characterized by different aromatic side-chain conformations at the RNA-binding surface allow for high- or low-affinity binding with functional implications. This study highlights a mechanism for RNA discrimination possibly common to multiple RRMs as several prominent members display a similar rearrangement of aromatic residues upon binding their targets.

Isothermal Titration Calorimetry

RNA recognition motif

Side chain

Sequence motif

10.1038/s41467-017-00631-3

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Citations (31)

Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts

Nature Communications (2018)

Olivier Duss Galina A. Stepanyuk Annette Grot Seán E. O’Leary Joseph D. Puglisi

Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the binding of ribosomal protein S15 to nascent RNA transcripts during early ribosome biogenesis. We observe stable binding of S15 to single RNAs immediately after transcription for the majority of the transcripts at 35 °C but for less than half at 20 °C. The remaining transcripts exhibit either rapid and transient binding or are unable to bind S15, likely due to RNA misfolding. Our work establishes the foundation for studying transcription and its coupled co-transcriptional processes, including RNA folding, ligand binding, and enzymatic activity such as in coupling of transcription to splicing, ribosome assembly or translation.

Transcription

10.1038/s41467-018-07423-3

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Citations (58)

Exploring the dynamics of messenger ribonucleoprotein-mediated translation repression

Biochemical Society Transactions (2024)

J Meyer Marco Payr Olivier Duss Janosch Hennig

Translational control is crucial for well-balanced cellular function and viability of organisms. Different mechanisms have evolved to up- and down-regulate protein synthesis, including 3′ untranslated region (UTR)-mediated translation repression. RNA binding proteins or microRNAs interact with regulatory sequence elements located in the 3′ UTR and interfere most often with the rate-limiting initiation step of translation. Dysregulation of post-transcriptional gene expression leads to various kinds of diseases, emphasizing the significance of understanding the mechanisms of these processes. So far, only limited mechanistic details about kinetics and dynamics of translation regulation are understood. This mini-review focuses on 3′ UTR-mediated translational regulation mechanisms and demonstrates the potential of using single-molecule fluorescence-microscopy for kinetic and dynamic studies of translation regulation in vivo and in vitro.

Translational regulation

Post-transcriptional regulation

10.1042/bst20231240

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Citations (0)

An Integrated Cell-Free Assay to Study Translation Regulation by Small Bacterial Noncoding RNAs

Methods in molecular biology (2018)

Erich Michel Olivier Duss Frédéric H.‐T. Allain

Translational regulation

Chloramphenicol acetyltransferase

Eukaryotic translation

10.1007/978-1-4939-7634-8_11

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Citations (3)

Tracking transcription-translation coupling in real-time

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Nusrat S. Qureshi Olivier Duss

Abstract A central question in biology is how macromolecular machines function cooperatively. In bacteria, transcription and translation occur in the same cellular compartment and can be physically and functionally coupled. While several recently published high-resolution structures of the ribosome-RNA polymerase (RNAP) complex provided first mechanistic insight into the coupling process, we do not know how these structural snapshots are placed along a dynamic reaction trajectory. Here, we reconstitute a complete active transcription-translation system and develop multi-color single-molecule fluorescence microscopy experiments to directly and simultaneously track transcription elongation, translation elongation and the physical and functional coupling between the ribosome and the RNAP in real-time. Our data show that the ribosome slows down while colliding with the RNAP and that coupling following a collision becomes less efficient. Unexpectedly, physical coupling can occur with hundreds of nucleotides of intervening mRNA between both machineries by mRNA looping, and increases in efficiency in presence of NusG. We detect active transcription elongation during mRNA looping and show that NusA-paused RNAPs can be activated by the ribosome by long-range physical coupling. We provide an alternative explanation on how the ribosome can rescue RNAP from frequent pausing without requiring collisions by a closely trailing ribosome. Our data mechanistically highlight an example of how macromolecular machines central to gene expression physically and functionally cooperate.

Transcription

Ribosome profiling

Molecular machine

10.1101/2023.12.07.570708

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Citations (5)